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covid-19, pandemic

After talking to @smarimc and thinking about it a bit, one metric importance became obvious: days-to-herd-immunity.

I'll explain in a sec; but first, let's make one thing clear: basically, we're all getting COVID-19 sooner or later. The fight is now about how many people get it *simultaneously*, or more importantly: how many people need to be simultaneously hospitalized.

Here's a decent explanation: https://medium.com/@ariadnelabs/social-distancing-this-is-not-a-snow-day-ac21d7fa78b4

So it's all about slowing down the spread. How much?

covid-19, pandemic

The data we need is: population of the country, current number of cases, and the estimated rate of new cases.

For #Iceland that's 364260 (population), 161 (current number of cases), 1.17 (rate of infection).

Herd immunity at 75% is 273195 people (infected, and those who already recovered). How long will it take?

Well, solve for x!

161*1.17^x = 273195

1.17^x = 273195/161

1.17^x ~= 1697

x=ln(1697)/ln(1.17) ~= 47 days

covid-19, pandemic

That also roughly means that the last day before herd immunity kicks in we can expect ~40.000 new infections. On that single day.

Now, if we lower the infection rate to 1.09, that we get 86 days to deal with it ( 🕶️ ), and the last day we get ~20.000 cases. Way more manageable.

This is all back-of-a-napkin math, obviously, there's a crap ton of variables that are not accounted for, plus it kinda makes most sense for isolated places like Iceland.

Still, eye-opening for me.

covid-19, pandemic

Few more takeaways from this:

1. 20k new cases on the idealized "day before herd immunity kicks in" still means that people who were infected before continue to need care. And 20k cases × 15% is 3k new patients needing hospital beds.

2. So... it would be better to spread it even further. If we go down to an infection rate of 1.04 we get peak at 10k cases, 1.5k new hospital patients. But that also means spreading it over 189 days!

3. Get used to it. It will take a long while.

covid-19, pandemic

Also, disclaimer:

1. This is all very naive, back-of-a-napkin math. Take it with a grain (or better yet, a whole spoon) of salt, do your own analysis.

2. I am not a healthcare professional and all of this can just as well be complete bullshit (if you know it is bullshit, let me know, eager to learn!).

3. The numbers are for Iceland. Plug in your own numbers. Here's my spreadsheet:

https://git.rys.io/rysiek/covid/blob/master/covid.ods

covid-19, pandemic

I think I know where the "I don't believe in herd immunity" stuff was coming from. Consider:

https://www.theguardian.com/commentisfree/2020/mar/15/epidemiologist-britain-herd-immunity-coronavirus-covid-19

What the UK gov't is doing is saying "we don't need all the protective measures because we want herd immunity as soon as possible". That's crap for all the reasons mentioned in the link.

My point: if we're lucky we can try to to slow infections down enough that the healthcare system can cope, and *hope* herd immunity kicks in; and here are the relevant numbers.

covid-19, pandemic

Okay, I started making a thing, because I had too much time on my hands (quarantine, yay!), and because I was annoyed about not having seen a decent place to get up-to-date stats on COVID-19 in different places:

It pulls the data from Wikipedia and applies to it the math I mentioned earlier in the thread.

Next steps are to implement:

1. comparisons between 2-3 countries

2. graphs similar to this one but updated with fresh data:

https://en.wikipedia.org/wiki/File:Epidemic_curve_update_18_march_20.png

covid-19, pandemic

It is now possible to:

- link directly to a particular infection site data: https://rys.io/covid/#iceland

- display data for several (as many as you like, I guess) infection sites side-by-side.

There are still bugs, and the styling is awkward right now. But perhaps it's useful.

covid-19, pandemic

Added the ability to link directly to data for a number of countries simultaneously, for example:

https://rys.io/covid/#iceland,united-states,turkey

covid-19, pandemic

Added graphs. These are still buggy (don't try to display more than 6 countries 😉 ), and the x axis is hardcoded, but I feel they're already kinda useful:

https://rys.io/covid/#iceland,united-states,turkey

Fun fact, Sweden for some reason is missing a day of data:

https://rys.io/covid/#sweden

Need to look at the data I guess.

covid-19, pandemic

@rysiek What's even more important (one might say: vitally/life-and-death important) is that most of us might already carry the virus and be contagious but not feel any effects (most of the very mild symptoms are barely noticeable). Here is a pretty effective chart to underline this fact: https://twitter.com/markwby/status/1238867143363567616

covid-19, pandemic

@rysiek It's its own form of Survivorship Bias: https://en.wikipedia.org/wiki/Survivorship_bias#In_the_military

covid-19, pandemic

@rysiek tfw. we'll want herd immunity to appear as late as possible

covid-19, pandemic

@wolf480pl exactly.

covid-19, pandemic

@rysiek counterintuitive AF

covid-19, pandemic

@rysiek how does that equation get more complicated with the rolling tourism turnover both for foreign visitors and icelanders going abroad?

covid-19, pandemic

@tomasino well, not sure. The data here is just "infection rate" and "current infections", so question is how we count the infected tourists?.. My feel is it changes the "herd immunity at infected and recovered" number, but it does not really complicate the math, since any new cases are already included in infection rate.

But need to ponder. :)

covid-19, pandemic

@rysiek for one thing it greatly changes the population figure. I have no idea how many tourists are in the country at any given point in time, though, especially right now. Hmm.

covid-19, pandemic

@rysiek is the number of cases number of infected people, or number of confirmed cases?

covid-19, pandemic

@wolf480pl number of all confirmed cases to date.

covid-19, pandemic

@rysiek

I think we should adjust for asymptomatic infections.

Eg. if 50% of infected people are asymptomatic, we reach herd immunity when all-confirmed-cases-so-far reaches ~35% of population.

covid-19, pandemic

@wolf480pl sure, but we also reach peak infections then. Question is: when we're saying that 15% of cases need hospital care and 5% of cases need critical care, is that of all cases or just symptomatic?

If all, that herd immunity at 35% of population having been symptomatic doesn't save the healthcare system...

covid-19, pandemic

@rysiek AFAIK we don't know how many asymptomatic cases there are, so I'd expect all relative numbers like hospitalization rate or mortality rate to be relative to the number of confirmed cases.

covid-19, pandemic

@rysiek

Btw. is China past its peak?

covid-19, pandemic

@wolf480pl probably not.

covid-19, pandemic

@rysiek

So the numbers on wikipedia are inaccurate?

covid-19, pandemic

@wolf480pl well, again, not a healthcare professional here. But, 80k cumulative cases is nowhere near herd immunity. And containing the virus outside of China is not really feasible, methinks.

So, sooner or later they will start getting more cases. If I were a betting man, my money would be on China preparing the capacity and procedures to gradually get herd immunity in place later.

covid-19, pandemic

@rysiek ok, but my questions are:

- are the numbers accurate? did they really stop at 80k confirmed cases? are they still testing?

- if so, how do you explain the numbers?

covid-19, pandemic

@wolf480pl I don't think I can explain the data. If they did stop at ~80k cases, good on them, but probably ended up using some serious authoritarian muscle.

covid-19, pandemic

@rysiek or 99.999% of cases are asymptomatic

covid-19, pandemic

@wolf480pl but you would still get other people getting infected from the asymptomatic cases.

covid-19, pandemic

@rysiek

Yes, but 99.999% of them would be asymptomatic.

It's all linear.

covid-19, pandemic

@wolf480pl fair. In such a case herd immunity would get there sooner, yeah.

re: covid-19, pandemic

@rysiek I guess the infection rate should also drop while the immunity is growing? With it being 1.17 now and around 1 or less at 70%-75%?

re: covid-19, pandemic

@ilja one can hope. but it might also go up, since herd immunity is still not there and there are way way more people and locations that are infected. So it becomes easier to catch COVID.

covid-19, pandemic

@rysiek

Stretch it by 2x once more and you may be outraced by a vaccine

re: covid-19, pandemic

I think you think is:

- The pandemic is impossible to contain. Eventually, most people will get infected. It's inevitable.

- As a result, herd immunity will develop

- We don't want herd immunity to develop too quickly, as that means too many people sick a the same time.

What UK thinks is:

- The pandemic is possible to contain. It may happen that significant portion of the population won't get infected.

- As a result, the pandemic may stop without herd immunity.

- We don't want to accidentally contain the pandemic, as that will mean no herd immunity.

So you both have the same setpoint, but a different estimate of the measured value.

You think we're undershooting, UK thinks we're overshooting.

re: covid-19, pandemic

@wolf480pl well, no, UK clearly thinks pandemic is not possible to contain and the reason why they want to go faster towards herd immunity is because they think there's going to be a "second wave" in the winter. It is rather clear they think it's not possible to contain.

re: covid-19, pandemic

@rysiek second wave implies not everyone gets infected this time...

re: covid-19, pandemic

@wolf480pl 75% is not everyone. Plus kids get born every day.

covid-19, pandemic

@rysiek

Now look at the numbers from China - they stopped at 80k confirmed cases. That means either:

- they're lying / stopped testing - you're right, also we lose

- they contained the epidemic - UK is right

- 99.999% cases were asymptomatic, they have herd immunity already - you're right, also we win

covid-19, pandemic

@wolf480pl again, UK gov clearly assumes pandemic is not containable. Not sure what's going on in China, but good on them. I do hope I'm wrong and that it's possible to contain SARS-CoV-2, but data from Italy and Spain does not bring me much hope of that.

covid-19, pandemic

@rysiek

I predict peak in Poland in 8 days

covid-19, pandemic

woah, half the us infected in less than a month? compare with france and italy (2.5 months), this should be eye-opening

covid-19, pandemic

@emptyfortress yeah, that's the whole point. It's hard for people to have an intuitive feel of what "exponential growth" means... Having the math done and data in front of their eyes helps, I hope.

covid-19, pandemic

@rysiek Something is misconfigured.

https://rys.io/covid/ works (with slash)

https://rys.io/covid doesn't work (without slash)

covid-19, pandemic

@desikn good catch, need to dive into nginx config and fix it. Thanks!

re: covid-19, pandemic

@rysiek Elegant. (Ok, I find it hard on the eyes, but at least it's aesthetic about it.) I like the crispness.

covid-19, pandemic

@rysiek I can't be bothered (and probably not technical enough) to decipher the GH code but do you scrape this data from Wikipedia or use a real-time Web source ?

covid-19, pandemic

@andyc Wikipedia is the source. It can be considered up-to-date down to, say, 6h periods. Stuff seems updated very quickly.

covid-19, pandemic

@rysiek A friend in Sweden tells me their policy right now is to only test ICU patients. She had every sign and was refused testing. So I wouldn't trust their numbers..

covid-19, pandemic

@cathal yeah, I don't really tryst any of the numbers fully. Even in #Iceland, where testing is very widespread and government response really dam solid there is always a number of asymptomatic people that will never get tested.

That being said, 60% of new confirmed cases in Iceland during the last ~24h or so were all people who were already quarantined. So, there is hope.

covid-19, pandemic

@rysiek you might want to look at Switzerland too, it thinks there are only 8 Swiss citizens :D

covid-19, pandemic

@emptyfortress hah, yeah. And some other country gas "(government)" as population figure. ;)

That's related to all the wonderful creative ways Wikipedia records population data for country pages. For example, I have not found a way to programmatically get the population figure for Iraq, even though it is right there on the Iraq wiki page.

*sigh*

But I am trying to fix what I can.

covid-19, pandemic

@emptyfortress Switzerland seems to work now. Thanks for the info though.

re: covid-19, pandemic

@rysiek Nice! Suggestion based on some article I read: when displaying multiple graphs, allow to set x=0, based on threshold value for y. For example: start graph at 150 confirmed cases.

re: covid-19, pandemic

@etam might make sense, and also might not be too difficult! Thanks for the suggestion.

re: covid-19, pandemic

@rysiek Another idea: Show graph on a linear scale with first and second derivative.

First derivative would show how many new cases were confirmed that day.

Second derivative would show how many more cases were confirmed, compared to previous day.

This would allow to see and compare how quickly it spreads in different countries.

(yes, I'm showing signs of Stockholm syndrome after learning calculus ;) )

rysiek the immune ☣@rysiek@mastodon.socialcovid-19, pandemic

Well, as mentioned by a lot of different sources, we need to slow it down such that the peak of infections is still something we can handle in the healthcare systems.

And the peak can be expected not that much sooner than when herd immunity kicks in. Let's say herd immunity kicks in at ~70-75% of population.

Well, now we have some numbers to work with!